try adding the path like so:

RewriteRule ^(.*)$ /site_directory/index.php?/$1 [L]

try adding the path like so:

RewriteRule ^(.*)$ /site_directory/index.php?/$1 [L]

EDIT:

Sometimes Apache can be set up different from server to server.

i. e. on DreamHost this would work

RewriteRule ^(.*)$ /site_directory/index.php?/$1 [L]

Where as on my Ubuntu VM or EngineHosting this works

RewriteRule ^(.*)$ /ci/index.php/$1 [L]

Try removing the "?" after index.php